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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3169_Nucleus_Fibroblast_pagetoid_Pericytes_Anulus_Mesenchymal_Skeletal
|full_id=C3169_Nucleus_Fibroblast_pagetoid_Pericytes_Anulus_Mesenchymal_Skeletal
|id=C3169
|id=C3169

Revision as of 16:02, 12 September 2012


Full id: C3169_Nucleus_Fibroblast_pagetoid_Pericytes_Anulus_Mesenchymal_Skeletal



Phase1 CAGE Peaks

Hg19::chr11:60640829..60640871,+p@chr11:60640829..60640871
+
Hg19::chr11:60640875..60640891,+p@chr11:60640875..60640891
+
Hg19::chr11:60640905..60640919,+p@chr11:60640905..60640919
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue3.83e-2561
striated muscle tissue3.83e-2561
myotome3.83e-2561
dermomyotome9.43e-2570
muscle tissue1.23e-2463
musculature1.23e-2463
musculature of body1.23e-2463
somite1.15e-2383
paraxial mesoderm1.15e-2383
presomitic mesoderm1.15e-2383
presumptive segmental plate1.15e-2383
trunk paraxial mesoderm1.15e-2383
presumptive paraxial mesoderm1.15e-2383
multilaminar epithelium1.24e-1982
trunk mesenchyme2.26e-16143
organism subdivision1.04e-13365
unilaminar epithelium2.99e-13138
multi-tissue structure6.71e-09347
cell layer9.63e-09312
trunk5.96e-08216
epithelium8.54e-08309
adipose tissue1.10e-0714
Disease
Ontology termp-valuen
ovarian cancer1.36e-0814


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOSL1#8061339.7135797163731.59554825631833e-050.000370140969217304
FOSL2#2355316.93020060456170.0002060162053171620.00242353305554394
MAX#414936.452555509007120.003721913834265510.0185827019283323
MYC#460935.22228187160940.007020843755740150.0293264768630063
REST#597839.650028716128020.001112636247114590.00765447711036168



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.